7/s simply means it clicks 7 times every second, not once every second.
Before level 30 it is 1 click every x seconds, after it is x clicks every second.
Do you realize that Handmade upgrade are just not worth buying them? I have lvl 31, next lvl costs 7455, so I more than 2 hours in order to gain some profit!
Hatchery mutation's working as intended. Don't dump all your mutagen into it early on - but later on, it scales better with hatcheries+expansions.